外显子比对率太低，参考基因组索引建立refFlat.txt文件有问题：
转录组索引
统计基因区域覆盖比例命令：
/share/work/biosoft/java/jre1.8.0_73/bin/java -jar /share/work/biosoft/picard/picard-tools-2.1.0/picard.jar CollectRnaSeqMetrics REF_FLAT=/share/work/database/ref/Saccharomyces_cerevisiae/Yeastgenome/refFlat.txt INPUT=/share/nas1/renzx/project/zx-20211019-394-1_ref_15jiaomu/ano/2.hisat2_stringtie/1.Mapping/3ts-30min/3ts-30min.bam OUTPUT=/share/nas1/renzx/project/zx-20211019-394-1_ref_15jiaomu/ano/2.hisat2_stringtie/2.Map_stat/3ts-30min.map_base.stat CHART_OUTPUT=/share/nas1/renzx/project/zx-20211019-394-1_ref_15jiaomu/ano/2.hisat2_stringtie/2.Map_stat/3ts-30min.Normalized_Distance_Along_Transcript.pdf STRAND_SPECIFICITY=NONE VALIDATION_STRINGENCY=LENIENT
refFlat.txt 文件行数过少导致出错：
查看原因：
生成该文件报错，导致生成的基因区域过少
gtfToGenePred -genePredExt saccharomyces_cerevisiae.gtf refFlat.tmp.txt
no exons defined for group HRA1, feature noncoding_exon (perhaps try -ignoreGroupsWithoutExons)
改进：
gtfToGenePred -genePredExt -ignoreGroupsWithoutExons saccharomyces_cerevisiae.gtf refFlat.tmp.txt
- 发表于 2022-01-13 09:57
- 阅读 ( 2270 )
- 分类：转录组
